CTSStagCount: Raw CAGE TSSs expression counts

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Raw CAGE TSSs expression counts

Description

Extracts the tag count for all detected TSSs in all CAGE datasets from CAGEexp objects.

Usage

CTSStagCountDF(object)

## S4 method for signature 'CAGEexp'
CTSStagCountDF(object)

CTSStagCountDA(object)

## S4 method for signature 'CAGEr'
CTSStagCountDA(object)

CTSStagCountGR(object, samples)

## S4 method for signature 'CAGEexp'
CTSStagCountGR(object, samples)

CTSStagCountSE(object)

## S4 method for signature 'CAGEexp'
CTSStagCountSE(object)

Arguments

object	A CAGEexp object.
samples	For CTSStagCountGR only: name(s) or number(s) identifying sample(s) or "all" to return a GRangesList of all the samples.

Value

Returns an object with number of CAGE tags supporting each TSS (rows) in every CAGE dataset (columns). The class of the object depends on the function being called:

• CTSStagCountDF: A DataFrame of Rle integers.

• CTSStagCountDA: A DelayedArray wrapping a DataFrame of Rle integers.

• CTSStagCountSE: A RangedSummarizedExperiment⁠containing a⁠DataFrameofRle' integers.

• CTSStagCountGR: A CTSS object (wrapping GRanges) containing a score column indicating expression values for a given sample, or a GRangesList of CTSS objects.

Author(s)

Vanja Haberle

Charles Plessy

See Also

getCTSS()

Other CAGEr accessor methods: CTSSclusteringMethod(), CTSScoordinatesGR(), CTSScumulativesTagClusters(), CTSSnormalizedTpmDF(), GeneExpDESeq2(), GeneExpSE(), consensusClustersGR(), expressionClasses(), genomeName(), inputFilesType(), inputFiles(), librarySizes(), sampleLabels(), seqNameTotalsSE(), tagClustersGR()

Examples

CTSStagCountDF(exampleCAGEexp)
 
CTSStagCountDA(exampleCAGEexp)

CTSStagCountGR(exampleCAGEexp, 1)
CTSStagCountGR(exampleCAGEexp, "all")
 
CTSStagCountSE(exampleCAGEexp)

charles-plessy/CAGEr documentation built on Nov. 4, 2023, 11:57 a.m.